1. Bioinformatics Computing
BCHB524 Lecture 0
BCHB524 - Edwards

2. Where to find me?
>> Teaching >> Bioinformatics Computing
BCHB524 - Edwards

3. Where to find me? Room 1217, Harris Building, 3300 Whitehaven St, NW
BCHB524 - Edwards
Room 1217, Harris Building, 3300 Whitehaven St, NW

4. Where to find me? Wisconsin Ave Shuttle
BCHB524 - Edwards
Wisconsin Ave Shuttle
Room W402, New Research Building

5. What about this course? Learn by doing. Learn by imitation.
Confront initial steep learning curve head-on.
Learn by imitation.
Change working programs for new functionality.
Learn by observation.
See cause-and-effect of program changes.
Learn by example.
Demonstrate with common, useful tasks.
Learn by idiom.
Use common programming abstractions.
BCHB524 - Edwards

6. What about this course? Lecture Computer-lab:
Monday, :30pm – 3:00pm, NRB W402
Wednesday, 1:30pm – 3:00pm, NRB W402
1-2 homework exercises at end of each lecture
Computer-lab:
Friday, 10am-12pm, Harris 1300
Required, for 5 credit students (Recommended)
Get help, work on homework, brainstorm with others
Weekly programming homework (60%)
Submit on Monday by noon, using canvas.
Term project (40%)
Significant bioinformatics analysis or software project
Presentation at end of semester.
BCHB524 - Edwards

7. Lectures Slides are posted to the web before each lecture,
Lectures will be recorded and available after lecture.
You must make sure you understand and can reproduce the examples I demonstrate in lecture…
…the homework presumes you’ll use the lecture examples as a starting point.
Go back over the material as soon as the lecture is over!
Predict how changes to the code will change the result.
BCHB524 - Edwards

8. Homework Due date is Monday at noon.
Solutions posted on Monday before class.
...so no credit for late homework!
Submit homework electronically to blackboard...
...canvas marks late submissions!
You may help each other and discuss, but no copy-and-paste!
No eyes on the screen!
BCHB524 - Edwards

9. Homework Write each exercise up as a mini-experiment.
Provide the result (the code).
Describe the method used and any tricky details.
Discuss the strengths and weaknesses of the solution.
Clarity, correctness, robustness, speed, other?
Document what you learned by carrying out the experiment.
BCHB524 - Edwards

10. Homework
Make sure you understand and can execute all of the examples from the lecture…
…otherwise, seek assistance.
Homework is strongly tied to the content of each lecture.
If you don't understand how, stop and think!
Learn from the solutions and critiques
If you don't understand the solutions or critiques, seek assistance.
BCHB524 - Edwards

11. You are responsible for your own learning!
You must
Do the homework!
Get help when you need it!
Work smart!
BCHB524 - Edwards

12. Virtual Machines
We will use a virtual machine as our programming environment
Consistent look and feel (Guest)
Regardless of your laptop / desktop (Host)
Get comfortable with VirtualBox
Use of Shared Folders
View options
Good bullet-point for your CV!
BCHB524 - Edwards

13. Linux Platform
We will use a Linux guest virtual machine as our programming environment
Free operating-system
Modest resource requirements
Our virtual machine is CentOS 5.11 based:
512Mb memory, 24Gb hard-drive
Common in bioinformatics and other scientific computing disciplines
Gain familiarity with command-line
Good bullet-point for your CV!
BCHB524 - Edwards